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Butternut Squash Mac and Cheese

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Butternut Squash Mac and Cheese, a healthier version of macaroni and cheese is so creamy and delicious, no one will ever guess it’s also good for you!

Butternut Squash Mac and Cheese
Butternut Squash Mac and Cheese

A few weeks ago I posted this Cauliflower “Mac” and Cheese recipe that swapped out pasta for cauliflower. Today I bring you this guilt-free mac and cheese recipe. Giving you all the comfort of the classic dish, but with an extra heaping of nutrients.

Butternut Squash Mac and Cheese

Hey there, I’m Heather K. Jones—I’m a dietitian, the nutrition expert for the Skinnytaste cookbooks, and the founder of the weight and wellness program, Feel Better Eat Better. If you struggle with emotional eating or weight anxiety, be sure to check out my free Masterclass by clicking RIGHT HERE. You’ll find out the exact steps I teach my clients to create lasting success from the inside-out, even if they’ve tried everything.

This guilt-free mac and cheese gives you all the comfort of the classic dish, but with an extra heaping of nutrients. Made with whole-wheat noodles, three cheeses (Gruyere, cheddar and Parmesan), shallots, and lots of good-for-your-body butternut squash… it’s cozy, creamy AND nourishing! This is a new staple for me and my sisters. Just add a big green salad and you have the perfect anytime meal.

butternut in the blenderwhite sauce with butternutwhite sauce with butternut squashButternut Squash Mac and CheeseButternut Squash Mac and Cheese

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Butternut Squash Mac & Cheese

4.73 from 85 votes
Butternut Squash Mac and Cheese, a healthier version of macaroni and cheese is so creamy and delicious, no one will ever guess it’s also good for you!
Course: Brunch, Lunch, Side Dish
Cuisine: American
Butternut Squash Mac and Cheese
Prep: 15 mins
Cook: 1 hr
Total: 1 hr 15 mins
Yield: 8 servings
Serving Size: 1 cup


  • Olive oil spray
  • Kosher salt
  • 1 pound cubed butternut squash
  • 10 ounces whole wheat elbow pasta
  • 1 ½ cups low sodium vegetable broth, divided
  • ½ teaspoon onion powder
  • ½ teaspoon garlic powder
  • ¼ cup panko breadcrumbs
  • 2 tablespoons freshly grated Parmesan cheese
  • 1 tablespoon unsalted butter
  • 1 medium shallot, minced
  • ¼ cup all-purpose flour
  • 2 cups skim milk
  • ½ cup shredded gruyere cheese
  • ½ cup shredded cheddar cheese
  • Chopped chives, optional, for garnish


  • Preheat oven to 375 degrees F. Spray a 9” x 11” glass baking dish with oil and set aside.
  • Bring a large pot of salted water to boil. Add squash and boil until tender, 5-6 minutes.
  • When fork tender, transfer squash with a slotted spoon to a blender.
  • Add pasta to boiling water and cook according to package directions. When cooked, drain and put back into the pot.
  • Meanwhile, add ½ cup vegetable broth, onion powder, garlic powder, 1 teaspoon salt and black pepper, to taste to the blender with the squash. Blend until smooth and creamy.
  • In a small bowl, combine breadcrumbs, Parmesan, ¼ teaspoon salt and pepper. Set aside.
  • Melt the butter in a medium sauce pot over medium heat. Add the shallots and sauté 2 minutes. Sprinkle the flour evenly over the shallots and cook another minute.
  • Add the remaining 1 cup broth and milk and whisk to combine. Bring sauce to a boil, then reduce heat to medium-low and cook 5 minutes, whisking frequently.
  • Remove pot from heat and whisk in cheese, pureed squash, 1 1/2 teaspoons salt and pepper.
  • Add sauce to noodles, gently mix to combine, then transfer mixture to prepared baking dish.
  • Sprinkle with breadcrumb mixture and bake 25 minutes. Switch oven to high broil and broil for 2-3 minutes, or until crumbs are starting to brown.

Last Step:

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Serving: 1 cup, Calories: 275 kcal, Carbohydrates: 43 g, Protein: 13 g, Fat: 7 g, Saturated Fat: 4 g, Cholesterol: 21 mg, Sodium: 462 mg, Fiber: 4.5 g, Sugar: 5 g


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170 comments on “Butternut Squash Mac and Cheese”

  1. Grade A: Took some time, but well worth it. I added a little more garlic powder, onion powder and add in dry mustard while decreasing the pepper.

  2. Hands down, probably one of the best Mac and Cheeses I have ever made. The hubs loved it too. I halved the recipe, and followed it pretty closely, except I added paprika and ground mustard to the rue. To save time for this week night meal, I made the butternut squash purée the day before and was able to get this all ready in 40 minutes.

  3. Delicious! I had a girlfriends lunch and made this with a tossed green salad. Everyone lived it.
    I made a few changes: added 1/4 cup extra broth to blender, added dry mustard, dijon mustard, and nutmeg to cheese sauce. Used combo of greyere, cheddar, and pepper jack Cheeses. Doubled amount of bread crumb topping. Baked 45 minutes (35 covered, 10 uncovered)

  4. This was delicious. We used whole milk and fontina cheese as it was a much better price than gruyere. Broiled at the end for an extra crispy top. Thought it was quite flavorful – maybe the flavor depends on the quality or freshness of the squash?

    Also delicious to add bacon!

  5. It’s good in theory but is way too bland. I had to add tarragon, sage, thyme, and basil in it to make it taste like anything. 

  6. This took a little more time to prepare than I normally put into weeknight meals, but WOW! It was worth it! I used Barilla Protein Plus Elbows and Reduced Fat Shredded Cheddar, which lowered the points for me. The only Gruyere I could find in my local market was smoked and that was a yummy plus, in my opinion. I had to be sure to divide this up into servings and store it right away or I would have eaten at least half of it in one sitting! Thanks for yet another great recipe!

  7. Avatar photo
    Elaine Dombrowski

    I liked this recipe, but, it seemed like a lot of effort. At first, I thought it was too ‘wet’, but, the oven took care of that nicely. Wondering if I can freeze it? 

  8. Can I make and freeze uncooked then bake? Or bake and freeze? Have anyone tried with chickpea noodles? THanks

  9. Has anyone tried making this with cauliflower instead of noodles? Just wondering about how much cauliflower and if there’s a strategy to keep it from getting too liquidy. 

  10. Can you prep it the night before and then cook in the oven the next day? Or would the noodles get too mushy?

  11. If I had puréed my butternut squash prior – how many cups would you suggest to use for the ingredients?

  12. Avatar photo
    Cidne Christensen

    Love this one definitely recommend adding hot sauce at least on top of it. If not just straight in the sauce

  13. Very flavorful! (Almost too salty and I was confused by hos much pepper… but turned out good!) Toddler ate it!

  14. This is the first time in ages I have found a recipe on this site that doesn’t have a button to link to WW personal points. Would it be possible to add one? 

  15. This is my favorite recipe for a healthy mac and cheese. It has so much flavor! It’s become a staple in my house for sure.
    Thanks for posting this Gina!

  16. Huge hit with my whole family. My husband was shocked when I told him it had butternut squash in the sauce! I oven baked it in a 9×13 pan, and added an three ounces of squash, and three ounces of noodles, so my proportion was slightly different from the recipe. I will be in our rotation

  17. Love this recipe! Have already made it 3 times within the past 2 months. People always ask for me to share the recipe

  18. Darn… really wanted to like this recipe, but it wasn’t salty or flavorful? I added 2x more cheese and a bit more salt, but it seemed like something ended up drowning out the mac’s taste 🙁 I just didn’t want to add even more sodium though,. I guess I need to tinker this to my liking.

    1. 1.5 teaspoons of salt are added in this recipe, in step 5 & 9. Cheese is salty, so when making a cheese substitute from butternut, adding enough salt is important to get that cheese-like flavor. I might try white miso next time.

      1. you could also try adding a tsp of Dijon mustard to the sauce to kick up the cheesiness. 

    2. I completely agree. I was really disappointed. All of that work and all those ingredients and it tasted like nothing. I’m followed the recipe to the T. Strange! 

  19. This dish is tasty and a fun combination of two fall staples. I paired it with a simple side salad to get some more veggies in (and also so that I wouldn’t be tempted to eat my weight in pasta).
    I tried to follow the recipe in general, but I did roast my butternut squash for added flavor and because I just couldn’t bring myself to boil them; it felt wrong. I also ended up using rigatoni instead of elbows just to make it look pretty. I used more cheese than called for because personally when I’m making mac’n’cheese, the healthiness of the dish isn’t my primary concern.
    Ultimately, my family and I enjoyed it and I would make it again. But it did feel like a labor of love and it turned my kitchen upside down. So, for me it is more of a special treat of a recipe than a weekday staple. Would recommend it though!

  20. Wow was this good! I made this with regular macaroni (to appease the husband) and subbed in chicken stock for veggie broth, plus oat milk instead of skim. We didn’t feel like we were eating ‘healthy’ Mac n cheese at all. It was very savory, and comfort food-y, nothing seemed lacking! I never would have guessed that I could have had such a delicious Mac n cheese with so little cheese/other heavy stuff.